[kepler-dev] RE: [SDM-SPA] Latest SPA Release (updated)

[Ilkay Altintas]

Hi Dan,

This sounds great.

I think we can directly use it with the generic web service actor as it
is available as a soap service. Developing a wrapper for it might be
unnecessary.

I will be happy to try it if you could provide me with the operation 
name and inputs for it.

What I saw from wsdl is that this web service uses almost all soap 
types. Currently the ws actor handles basic xsd types and some array 
types. It should be possible to use it as is with the extension to the 
web service actor for the map array.

Ilkay



-----Original Message-----
From: sdm-dev-admin at sdsc.edu [mailto:sdm-dev-admin at sdsc.edu]On Behalf Of
dcolonn at ncsu.edu
Sent: Monday, March 08, 2004 10:10 AM
To: buttler1 at llnl.gov
Cc: Daniel Colonnese; sdm-dev at sdsc.edu; sdm at renoir.csc.ncsu.edu;
kepler-dev at ecoinformatics.org; xin2 at llnl.gov
Subject: Re: [SDM-SPA] Latest SPA Release (updated)



Soaplab is hosting a WSDL service for tfscan.  The SoapLab developer,
Martin Senger, just updated the TRANSFAC data on his end.

I was the first on to use this service, so we worked out a few minor
problems; now it's a working web service.

The tfscan WSDL is at:

http://industry.ebi.ac.uk/soaplab/wsdl/nucleic_transcription__tfscan.wsdl


Since you think it is a possible replacement for the old service,  I'll
get to work on wrapping a ptolemy actor for this tfscan.

And I'll keep my eyes open for a computer scientist who's fluent in German.


-Dan


> Hi Daniel,
>
> I believe that this would be a suitable replacement for Transfac.  My
> understanding is that to use this tool, you need to download the data
> directly from the transfac site.  Did you have a chance to check that
> the transfac FTP site is still available?  When I tried, the response
> just hung.  If we could set up the service locally (either as an
> executable to include in a distribution, or as a Web service) it would
> seem to have some value. Perhaps I misunderstood your intent though; did
> you mean to say that they (the developers of EMBOSS) would be willing to
> host a WSDL service for the world to access?
>
> Many of the services provided by the EMBOSS tool suite that includes
> tfscan would make useful additions to the bioinformatics side of
> Kepler.  Once we get the system set up here for Matt, we will explore
> what would be of value to him.
>
> As a side note, it turns out that Matt Coleman has a seat license for
> genomatix.de, which includes a transfac web interface.  So, it should be
> possible to develop an actor that uses this information.  Perhaps one of
> us could contact this company directly to see if they would be willing
> to make their services available as a Web service for licensed users.
> This should save us some implementation/screen scraping effort and
> sounds like a reasonable approach for the company. Any volunteers?
>
> Two last pieces of information from my meeting with Matt today:
> He is going to be on travel for most of March.  We will meet with him
> again on the 26th to show him the workflow system.
> Also, in the future, he would be interested in joining our monthly SPA
> meeting, or perhaps other ad hoc meetings, to discuss the state of the
> system and what could be done to best meet his needs.
>
> Dave
>
> Daniel Colonnese wrote:
>
>>Dear All,
>>
>>I have found a potential TRANSFAC service. It is a free service offered
>>by European Bioinformatics Institute.  I have been in touch with the
>>service author and they are cooperative and willing to work us.
>>
>>Before I turn this into a Ptolemy actor, I need some help to determine
>>whether this service is suitable replacement for the previous transfac
>>service.
>>
>>The service is an interface to the TFSCAN program.  Here is a
>>description of that program
>>
>>http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/tfscan.html
>>
>>Let's schedule a meeting for Monday or Tuesday where Matt can help us
>>decide.
>>
>>Please let me know,
>>
>>Dan
>>
>>
>>
>>
>>
>>
>>
>